The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. The current genome-wide methods for detecting histone modifications are based on DNA microarrays, which contain a fraction of coding sequences and intergenic regions. True genome-wide analysis of histone modifications requires DNA arrays containing all the genomic sequences, which are not available for the human genome. We developed a non-biased genome-wide mapping technique (GMAT) by the combination of SAGE (Serial Analysis of Gene Expression) and chromatin immunoprecipitation (ChIP) protocols to analyze histone modifications of the entire genome. We have applied this technique to analyze the high-resolution genome-wide distribution of K9/K14 diacetylated histone H3 in resting and activated human T cells. Our data indicate that while the promoter regions are highly acetylated, there are no sustained high levels of acetylation in transcribed regions. Islands of acetylation are located in the intergenic and transcribed regions. Of the 46,813 acetylation islands identified in this study, 66% are associated with conserved noncoding sequences (CNSs) and many are correlated with known regulatory elements in T cells. TCR signaling induces 4,045 new acetylation islands that may mediate the global chromatin remodeling and gene activation. We present data to show that Acetylation Islands are functional regulatory elements. Our studies show that chromatin accessibility and gene expression of a genetic domain in mammalian cells is correlated with hyperacetylation of promoters and other regulatory elements but not with uniform hyperacetylation of the whole domain. We propose that the acetylation islands are epigenetic marks which allow prediction of functional regulatory elements.